Variant report

Variant	rs1477164
Chromosome Location	chr2:39685772-39685773
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39680725..39683099-chr2:39684790..39686742,2	MCF-7	breast:
2	chr2:39684833..39686565-chr2:39689328..39692216,2	MCF-7	breast:
3	chr2:39685470..39688702-chr2:39694435..39696630,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10169391	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10170424	0.89[AFR][1000 genomes]
rs10170604	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10173556	0.89[AFR][1000 genomes]
rs10175333	0.81[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10181650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1035232	0.89[AFR][1000 genomes]
rs10865150	0.86[YRI][hapmap]
rs10865152	0.89[AFR][1000 genomes]
rs11124676	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs11124677	0.84[AFR][1000 genomes]
rs11124679	0.93[AFR][1000 genomes]
rs11124681	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12614034	0.82[AFR][1000 genomes]
rs12622941	0.82[YRI][hapmap]
rs12712641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13028561	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1468902	0.81[AFR][1000 genomes]
rs1474424	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1922827	0.94[YRI][hapmap];0.89[AFR][1000 genomes]
rs2005892	0.87[AFR][1000 genomes]
rs2056654	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2111382	0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2160661	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2178762	0.92[AFR][1000 genomes]
rs2193422	0.89[AFR][1000 genomes]
rs2373536	0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2708224	0.83[AMR][1000 genomes]
rs2888598	0.92[AFR][1000 genomes]
rs3755178	0.94[YRI][hapmap]
rs4670934	0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670935	0.81[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4670936	0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6419603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544222	0.90[AFR][1000 genomes]
rs6544223	0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544228	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6717792	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6718134	0.83[AFR][1000 genomes]
rs6724393	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730902	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732611	0.88[AFR][1000 genomes]
rs6741312	0.82[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742170	0.89[AFR][1000 genomes]
rs6743041	0.94[YRI][hapmap]
rs6756183	0.92[YRI][hapmap]
rs6759495	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6760382	0.89[AFR][1000 genomes]
rs7578136	0.87[AFR][1000 genomes]
rs7579414	0.83[AFR][1000 genomes]
rs7582160	0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591102	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7595041	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7601700	0.86[YRI][hapmap]
rs7603392	0.81[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7604047	0.82[AFR][1000 genomes]
rs7608153	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39665200-39696000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39665600-39694600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:39665600-39694800	Weak transcription	Pancreas	Pancrea
4	chr2:39666200-39696600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:39667000-39694600	Weak transcription	HSMMtube	muscle
6	chr2:39667200-39694600	Weak transcription	NHLF	lung
7	chr2:39667200-39694800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:39667200-39696400	Weak transcription	Fetal Heart	heart
9	chr2:39667400-39694600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:39667400-39694600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:39668200-39694800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:39668200-39696800	Weak transcription	Right Ventricle	heart
13	chr2:39675000-39696400	Weak transcription	Fetal Kidney	kidney
14	chr2:39675200-39686000	Weak transcription	NHDF-Ad	bronchial
15	chr2:39675400-39694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:39677200-39687400	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:39678000-39696800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:39678200-39694600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:39681000-39686200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:39682200-39692000	Weak transcription	Fetal Lung	lung
21	chr2:39682200-39695600	Weak transcription	Fetal Brain Male	brain
22	chr2:39682400-39686000	Weak transcription	Liver	Liver
23	chr2:39682400-39694600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr2:39682600-39685800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:39682600-39687200	Weak transcription	Adipose Nuclei	Adipose
26	chr2:39682600-39694800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:39682600-39695600	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:39682600-39695800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:39682800-39694400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:39682800-39694600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:39683000-39694600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:39683200-39685800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:39683200-39686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:39683200-39694400	Weak transcription	HepG2	liver
35	chr2:39683200-39694600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:39683200-39694600	Weak transcription	Ovary	ovary
37	chr2:39683200-39694800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:39683400-39694800	Weak transcription	NH-A	brain
39	chr2:39684400-39686400	Strong transcription	HSMM	muscle
40	chr2:39684600-39686000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:39684600-39687600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:39684800-39685800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:39684800-39686200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr2:39684800-39687400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:39685000-39686200	ZNF genes & repeats	Aorta	Aorta
46	chr2:39685200-39686600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:39685200-39688200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr2:39685200-39692600	Weak transcription	Placenta	Placenta
49	chr2:39685200-39694800	Weak transcription	Gastric	stomach
50	chr2:39685200-39705000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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